2Y1I | pdb_00002y1i

Crystal structure of a S-diastereomer analogue of the spore photoproduct in complex with fragment DNA polymerase I from Bacillus stearothermophilus

• PDB DOI: https://doi.org/10.2210/pdb2Y1I/pdb
• NAKB: 2Y1I

• Classification: TRANSFERASE/DNA
• Organism(s): Geobacillus stearothermophilus, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-12-08 Released: 2011-07-27 
• Deposition Author(s): Heil, K., Schneider, S., Mueller, M., Kneuttinger, A.C., Carell, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.78 Å
• R-Value Free: 
  0.273 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.226 (Depositor) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: experimental

Literature

Crystal Structures and Repair Studies Reveal the Identity and the Base-Pairing Properties of the Uv-Induced Spore Photoproduct DNA Lesion.

Heil, K., Kneuttinger, A.C., Schneider, S., Lischke, U., Carell, T.

(2011) Chemistry 17: 9651

• PubMed: 21780197 
• DOI: https://doi.org/10.1002/chem.201100177
• Primary Citation Related Structures: 
  2Y1I, 2Y1J


• PubMed Abstract: 
  

  UV light is one of the major causes of DNA damage. In spore DNA, due to an unusual packing of the genetic material, a special spore photoproduct lesion (SP lesion) is formed, which is repaired by the enzyme spore photoproduct lyase (Spl), a radical S-adenosylmethionine (SAM) enzyme. We report here the synthesis and DNA incorporation of a DNA SP lesion analogue lacking the phosphodiester backbone. The oligonucleotides were used for repair studies and they were cocrystallized with a polymerase enzyme as a template to clarify the configuration of the SP lesion and to provide information about the base-pairing properties of the lesion. The structural analysis together with repair studies allowed us to clarify the identity of the preferentially repaired lesion diastereoisomer.

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Organizational Affiliation: 
• Center for Integrated Protein Science (CiPSM) at the Department of Chemistry, Ludwig-Maximilians-University, Munich, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 72.41 kDa 
• Atom Count: 5,068 
• Modeled Residue Count: 600 
• Deposited Residue Count: 600 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA POLYMERASE I	A	580	Geobacillus stearothermophilus	Mutation(s): 0  EC: 2.7.7.7
UniProt
Find proteins for E1C9K5 (Geobacillus stearothermophilus) Explore E1C9K5  Go to UniProtKB:  E1C9K5

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*GP*AP*CP*CP*AP*AP*CP*CP*CP*TP)-3'	B	10	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*AP*GP*GP*GP*PBTP*THM*GP*GP*TP*CP)-3'	C	10	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.78 Å
• R-Value Free:  0.273 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.226 (Depositor) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.669	α = 90
b = 93.793	β = 90
c = 107.101	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-27 
Deposition Author(s): Heil, K., Schneider, S., Mueller, M., Kneuttinger, A.C., Carell, T.

Revision History  

• Version 1.0: 2011-07-27
  Type: Initial release
  
• Version 1.1: 2011-11-02
  Changes: Database references
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description